Alexsavio scripts - Historial de revisiones

Alexsavio en 09:35 24 jul 2012

2012-07-24T09:35:44Z

← Revisión anterior		Revisión del 11:35 24 jul 2012
Línea 1:		Línea 1:
			#!/usr/bin/python

			#-------------------------------------------------------------------------------
			#License GPL v3.0
			#Author: Alexandre Manhaes Savio <alexsavio@gmail.com>
			#Grupo de Inteligencia Computational <www.ehu.es/ccwintco>
			#Universidad del Pais Vasco UPV/EHU
			#Use this at your own risk!
			#-------------------------------------------------------------------------------

			import sys
			import argparse
			import numpy as np
			import nibabel as nib
			import scipy.ndimage as scn

			#-------------------------------------------------------------------------------
			def set_parser():
			parser = argparse.ArgumentParser(description='Empties each ROI in the 3D input volume and saves the result in the output volume.')
			parser.add_argument('-i', '--in', dest='input', required=True, help='input file')
			parser.add_argument('-o', '--out', dest='output', required=True, help='output file')
			return parser

			#-------------------------------------------------------------------------------
			def add_extension_if_needed (fpath, ext, check_if_exists=False):

			if fpath.find(ext) < 0:
			fpath += ext

			if check_if_exists:
			if not os.path.exists (fpath):
			err = 'File not found: ' + fpath
			raise IOError(err)

			return fpath

			#-------------------------------------------------------------------------------
			def main(argv=None):

			parser = set_parser()

			try:
			args = parser.parse_args ()
			except argparse.ArgumentError, exc:
			print (exc.message + '\n' + exc.argument)
			parser.error(str(msg))
			return 0

			ifname = args.input.strip()
			ofname = args.output.strip()

			ofname = add_extension_if_needed(ofname, '.nii.gz')

			aff = nib.load(ifname).get_affine()
			vol = nib.load(ifname).get_data()
			out = np.zeros(vol.shape, dtype=vol.dtype)

			if vol.ndim == 2:
			kernel = np.ones([3,3], dtype=int)
			elif vol.ndim == 3:
			kernel = np.ones([3,3,3], dtype=int)
			elif vol.ndim == 4:
			kernel = np.ones([3,3,3,3], dtype=int)

			vals = np.unique(vol)
			vals = vals[vals != 0]

			for i in vals:
			roi = vol == i
			hits = scn.binary_hit_or_miss (roi, kernel)
			roi[hits] = 0
			out[roi > 0] = i

	== FSL Tools ==		== FSL Tools ==

Alexsavio: /* create_tissue_prob_maps.sh */

2009-01-15T14:42:18Z

create_tissue_prob_maps.sh

← Revisión anterior		Revisión del 16:42 15 ene 2009
Línea 149:		Línea 149:
	rm $temp_csf		rm $temp_csf
	rm $temp_grey		rm $temp_grey

	echo $cont files processed.		echo $cont files processed.

Alexsavio: /* FSL Tools */

2009-01-15T14:42:04Z

FSL Tools

← Revisión anterior		Revisión del 16:42 15 ene 2009
Línea 1:		Línea 1:
	== FSL Tools ==		== FSL Tools ==

	~~'''~~create_mean_template.sh~~'''~~		=== create_mean_template.sh ===

	#!/bin/bash		#!/bin/bash

Alexsavio: /* create_tissue_prob_maps.sh */

2009-01-15T14:41:50Z

create_tissue_prob_maps.sh

← Revisión anterior		Revisión del 16:41 15 ene 2009
Línea 60:		Línea 60:

	#!/bin/bash		#!/bin/bash

	subjs_root=../Female/segmented		subjs_root=../Female/segmented
	target_dir=$PWD		target_dir=$PWD

Alexsavio: /* FSL Tools */

2009-01-15T14:41:39Z

FSL Tools

← Revisión anterior		Revisión del 16:41 15 ene 2009
Línea 54:		Línea 54:
	rm -f $temp		rm -f $temp

			echo $cont files processed.


			=== create_tissue_prob_maps.sh ===

			#!/bin/bash

			subjs_root=../Female/segmented
			target_dir=$PWD
			cd $subjs_root

			cont=0

			white_map=white.nii.gz
			grey_map=grey.nii.gz
			csf_map=csf.nii.gz

			temp_white=temp_white.nii.gz
			temp_grey=temp_grey.nii.gz
			temp_csf=temp_csf.nii.gz

			if [ -f $white_map ]
			then
			rm $white_map
			fi

			if [ -f $grey_map ]
			then
			rm $grey_map
			fi

			if [ -f $csf_map ]
			then
			rm $csf_map
			fi

			ls *hdr \| while read vol;
			do
			cont=$(($cont + 1))

			echo $cont - $vol

			#obtain white matter
			fslmaths $vol -thr 3 -bin $temp_white

			#obtain csf
			fslmaths $vol -uthr 1 -bin $temp_csf

			#obtain grey
			fslmaths $vol -thr 2 $temp_grey
			fslmaths $temp_grey -uthr 2 -bin $temp_grey

			#sum white
			if [ -f $white_map ]
			then
			fslmaths $white_map -add $temp_white $white_map
			else
			cp $temp_white $white_map
			fi

			if [ -f $grey_map ]
			then
			fslmaths $grey_map -add $temp_grey $grey_map
			else
			cp $temp_grey $grey_map
			fi

			if [ -f $csf_map ]
			then
			fslmaths $csf_map -add $temp_csf $csf_map
			else
			cp $temp_csf $csf_map
			fi
			done

			cont=`ls *hdr \| wc -l`

			#normalize
			fslmaths -dt float $white_map -div $cont $white_map -odt float
			fslmaths -dt float $grey_map -div $cont $grey_map -odt float
			fslmaths -dt float $csf_map -div $cont $csf_map -odt float

			#smooth
			fslmaths $white_map -kernel gauss 2 -fmean $white_map
			fslmaths $grey_map -kernel gauss 2 -fmean $grey_map
			fslmaths $csf_map -kernel gauss 2 -fmean $csf_map

			#move to target directory
			mv $white_map $target_dir
			mv $grey_map $target_dir
			mv $csf_map $target_dir

			rm $temp_white
			rm $temp_csf
			rm $temp_grey

	echo $cont files processed.		echo $cont files processed.

Alexsavio: /* FSL Tools */

2009-01-15T14:39:46Z

FSL Tools

← Revisión anterior		Revisión del 16:39 15 ene 2009
Línea 1:		Línea 1:
	== FSL Tools ==		== FSL Tools ==

	create_mean_template.sh		'''create_mean_template.sh'''

	#!/bin/bash		#!/bin/bash

	#This script reads all images from the $subjs_root directory and creates a new smoothed image with the mean intensity value of all the images.		#This script reads all images from the $subjs_root directory and creates a new smoothed image with the mean intensity value of all the images.

	subjs_root=../Female/original		subjs_root=../Female/original
	target_dir=$PWD		target_dir=$PWD

Alexsavio: /* Alex Scripting */

2009-01-15T14:39:20Z

Alex Scripting

← Revisión anterior		Revisión del 16:39 15 ene 2009
Línea 1:		Línea 1:
	~~== Alex Scripting ==~~		== FSL Tools ==

	=== FSL Tools ===

	create_mean_template.sh		create_mean_template.sh

	#!/bin/bash		#!/bin/bash

			#This script reads all images from the $subjs_root directory and creates a new smoothed image with the mean intensity value of all the images.

	subjs_root=../Female/original		subjs_root=../Female/original
	target_dir=$PWD		target_dir=$PWD

Alexsavio en 14:37 15 ene 2009

2009-01-15T14:37:43Z

Página nueva

== Alex Scripting ==

=== FSL Tools ===

create_mean_template.sh

#!/bin/bash

subjs_root=../Female/original
target_dir=$PWD
cd $subjs_root

cont=0
subj_num=`ls *t88_gfc*hdr | wc -l`

template=template.nii.gz
temp=temp.nii.gz

if [ -f $template ]
then
rm -f $template
fi

if [ -f $temp ]
then
rm -f $temp
fi

ls *hdr | while read vol;
do
cont=$(($cont + 1))

echo $cont - $vol

if [ -f $template ]
then
tmp=`fslstats $vol -r`
max_intensity=${tmp:`expr index "$tmp" ' '`:${#tmp}}
fslmaths -dt double $vol -div $subj_num $temp
fslmaths -dt double $temp -add $template $template -odt double
else
tmp=`fslstats $vol -r`
max_intensity=${tmp:`expr index "$tmp" ' '`:${#tmp}}
fslmaths -dt double $vol -div $subj_num $template
fi
done

cont=`ls *hdr | wc -l`

#smooth
fslmaths $template -kernel gauss 2 -fmean $template

mv $template $target_dir

rm -f $temp

echo $cont files processed.